Use of the glass electrode in deuterium oxide and the relation between the standardized pD (paD) scale and the operational pH in heavy water

Covington, A. K.; Paabo, Maya; Robinson, R. A.; Bates, Roger G.

doi:10.1021/ac60260a013

Cited by 651 publications

(430 citation statements)

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“…The pH was calculated from the measured pD value by using the relationship pH = pDÀ0.40. [55] ESI mass spectra were performed with a ESI Mass TSQ 700 FINNIN-GAM by using the free ligand D, which was obtained by extraction in chloroform of an aqueous alkaline solution prepared from D·4 HBr·EtOH.…”

Section: Methodsmentioning

confidence: 99%

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

Bazzicalupi

Bencini

Bianchi

et al. 2007

Chemistry A European J

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The new bifunctional molecule 3,6‐diamine‐9‐[6,6‐bis(2‐aminoethyl)‐1,6‐diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal‐complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal‐complexing constants, optical properties and self‐aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped‐flow technique. Static measurements show biphasic behaviour for both D–DNA and [ZnD]–DNA systems; this reveals the occurrence of two different binding processes depending on the polymer‐to‐dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped‐flow, circular dichroism and supercoiled‐DNA unwinding experiments corroborate the proposed mechanism. Molecular‐modelling studies support the intercalative process and evidence the influence of NH+⋅⋅⋅O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.

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Section: Methodsmentioning

confidence: 99%

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

Bazzicalupi

Bencini

Bianchi

et al. 2007

Chemistry A European J

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“…The pH of assay mixtures in H,O were determined with commercially available glass electrodes standardized with buffer solutions in H,O. The pD of assay mixtures in D,O was measured by using the same calibrated electrode taking into account that pD = pH+0.41, where pH is the pH meter reading (Covington et al, 1968;Quinn and Sutton, 1991).…”

Section: Methodsmentioning

confidence: 99%

Hydrogen Isotope Effects in the Reactions Catalyzed by H₂‐forming N⁵,N¹⁰‐Methylenetetrahydromethanopterin Dehydrogenase from Methanogenic Archaea

Klein

Hartmann

Thauer

1995

European Journal of Biochemistry

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H,-forming N',N"'-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea, which is a novel hydrogenase containing neither nickel nor iron-sulfur clusters, catalyzes the reversible reduction of N5,N"'-methenyltetrahydomethanopterin (CH=H,MPT.') with H, to N',N"'-methylenetetrahydromethanopterin (CH,=H,MPT) and a proton (AGO' = -5.5 kJ/mol). The enzyme also catalyzes a CH-H,MPT+-dependent H,/H' exchange. We report here on kinetic deuterium isotope effects in these reactions. When CH=H,MPT' reduction was performed with DZ instead of H2, V,,,., and the K,,, did not change. A primary isotope effect of 1 was found at all pH and temperatures tested and independent of whether H,O or DZO was the solvent. The findings indicate that a step other than the activation of H, was rate-determining in CH=H,MPT+ reduction with H,. This was substantiated by the observation that also the CH=H,MPT+-dependent H,/H+ exchange reaction did not exhibit an appreciable deuterium isotope effect. V,,,,, for CH,=H,MPT dehydrogenation to CH-H,MPT+ and H2 was only 2-3 times higher than for CD2=H,MPT dehydrogenation to CD-H,MPT' and HD. Such a small primary isotope effect indicates that the breakage of the C-H bond in the methylene group of CH2=H,MPT was only rate-limiting when hydrogen was substituted by a deuterium.

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“…pH was measured with a Radiometer PHM63 digital pH-meter equipped with a 5 mm combination electrode. The direct reading pH* from a 2 H2O solution (with the pH meter calibrated with standard H2O buffers) was converted to thermodynamically meaningful pD values according to pD = pH* + 0.41 (Covington et al, 1968). Desired pD values were obtained by adding small amounts of 5 M HCl or 5 M KOH to the protein solutions.…”

Section: Protein Solutionsmentioning

confidence: 99%

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

Денисов

Halle

1995

Journal of Molecular Biology

162

177

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Water oxygen-17 spin relaxation was used to study hydration and dynamics Condensed Matter Magnetic Resonance Group, Chemical of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and ubiquitin in aqueous solution. The frequency dispersion of the longitudinal Center, Lund University P. O. Box 124, S-22100 Lund and transverse relaxation rates was measured over the Larmor frequency Sweden range 2.6 to 49 MHz in the pD range 2 to 11 at 27°C. While the protein-induced relaxation enhancement was similar for the two proteins at high frequencies, it was an order of magnitude smaller for ubiquitin than for BPTI at low frequencies. This difference was ascribed to the abscence, in ubiquitin, of highly ordered internal water molecules, which are known to be present in BPTI and in most other globular proteins. These observations demonstrate that the water relaxation dispersion in protein solutions is essentially due to a few structural water molecules buried within the protein matrix, but exchanging rapidly with the external water. The relaxation data indicate that the internal water molecules of BPTI exchange with bulk water on the time-scale 10 −8 to 10 −6 second thus lowering the recently reported upper bound on the residence time of these internal water molecules by four orders of magnitude, and implying that local unfolding occurs on the submicrosecond time-scale. The water molecules residing at the surface of the two proteins were found to be highly mobile, with an average rotational correlation time of approximately 20 picoseconds. For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. We believe that the present results resolve the long-standing controversy regarding the mechanism behind the spin relaxation dispersion of water nuclei in protein solutions, thus establishing oxygen-17 relaxation as a powerful tool for studies of structurally and functionally important water molecules in proteins and other biomolecules.

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Use of the glass electrode in deuterium oxide and the relation between the standardized pD (paD) scale and the operational pH in heavy water

Cited by 651 publications

References 20 publications

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

Hydrogen Isotope Effects in the Reactions Catalyzed by H₂‐forming N⁵,N¹⁰‐Methylenetetrahydromethanopterin Dehydrogenase from Methanogenic Archaea

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

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Use of the glass electrode in deuterium oxide and the relation between the standardized pD (paD) scale and the operational pH in heavy water

Cited by 651 publications

References 20 publications

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

Hydrogen Isotope Effects in the Reactions Catalyzed by H2‐forming N5,N10‐Methylenetetrahydromethanopterin Dehydrogenase from Methanogenic Archaea

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

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Hydrogen Isotope Effects in the Reactions Catalyzed by H₂‐forming N⁵,N¹⁰‐Methylenetetrahydromethanopterin Dehydrogenase from Methanogenic Archaea